ArticleGigaScience2018
A benchmark study of k-mer counting methods for high-throughput sequencing.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
43 citing papers in PubMed.
- Evolutionary Patterns of the Genes Involved in the Integrity and Segregation of Chromosomes in Sawflies (Hymenoptera: Symphyta).Ecology and evolution · 2026Article
- Chromosome-Scale Haplotype Genome Assemblies for the Australian Mango 'Kensington Pride' and a Wild Relative, Mangifera laurina, Provide Insights Into Anthracnose-Resistance and Volatile Compound Biosynthesis Genes.Plant biotechnology journal · 2026Article
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- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Genome survey and evolutionary analysis of 8 Lamprotula species: SSR profiling, mitochondrial characterization, and population dynamics inference.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Efficient Storage and Analysis of Genomic Data: A k-mer Frequency Mapping and Image Representation Method.Interdisciplinary sciences, computational life sciences · 2025Article
- The genomes of the most diverse AA genome rice species provide a resource for rice improvement and studies of rice evolution and domestication.BMC genomics · 2025Article
- Poplar: a phylogenomics pipeline.Bioinformatics advances · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- The genomes of Australian wild limes.Plant molecular biology · 2024Article
- Short-time AOIs-based representative scanpath identification and scanpath aggregation.Behavior research methods · 2024Article
- A chromosome-level genome of mango exclusively from long-read sequence data.The plant genome · 2024Article
- The genome of Citrus australasica reveals disease resistance and other species specific genes.BMC plant biology · 2024Article
- APIPred: An XGBoost-Based Method for Predicting Aptamer-Protein Interactions.Journal of chemical information and modeling · 2024Article
- Space-efficient computation of k-mer dictionaries for large values of k.Algorithms for molecular biology : AMB · 2024Article
- Chemical unclonable functions based on operable random DNA pools.Nature communications · 2024Article
- Review
- Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species.BMC genomics · 2023Article
- Haplotype resolved chromosome level genome assembly ofHorticulture research · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid development of high-throughput sequencing technologies means that hundreds of gigabytes of sequencing data can be produced in a single study. Many bioinformatics tools require counts of substrings of length k in DNA/RNA sequencing reads obtained for applications such as genome and transcriptome assembly, error correction, multiple sequence alignment, and repeat detection. Recently, several techniques have been developed to count k-mers in large sequencing datasets, with a trade-off between the time and memory required to perform this function. We assessed several k-mer counting programs and evaluated their relative performance, primarily on the basis of runtime and memory usage. We also considered additional parameters such as disk usage, accuracy, parallelism, the impact of compressed input, performance in terms of counting large k values and the scalability of the application to larger datasets.We make specific recommendations for the setup of a current state-of-the-art program and suggestions for further development.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.